Peptide deformylase (PDF) has been long recognized as important in protein synthesis. Removal of the formyl moiety on the N-terminal methionine of nascent proteins by PDF is a necessary activity for prokaryotic cell viability (Mazel et al., Embo. J. 1994, 13, 914-923). The central role of PDF in bacterial protein synthesis has led to significant efforts to discover antibiotics that selectively target bacterial PDFs (Howard et al., J. Med. Chem. 2004, 47, 6669-6672; Leeds et al., Current Opinion in Pharmacology 2006, 6, 445-452). PDF inhibitors are a promising drug class, as has been demonstrated by the broad spectrum activity in vitro against drug resistant bacterial strains of the clinical drug candidates LBM415 (Watters et al., J. Antimicrob. Chemother. 2006, 57, 914-923) and BB-83698 (Lofland et al., J. Antimicrob. Chemother. 2004, 53, 664-668). The PDF inhibitor BB-83698 has been proposed as a tuberculosis treatment (Teo et al., Antimicrob. Agents Chemother. 2006, 50, 3665-3673).
PDF activity was not believed to be important in eukaryotic cells until recently because nuclear encoded proteins are not N-formylated (Serero et al., J. Biol. Chem. 2003, 278, 52953-52963). However, in eukaryotes, mitochondrial protein synthesis involves the formylation and deformylation of proteins, as evidenced by the presence of the enzymatic machinery to perform these activities in mammals and plants, among other eukaryotes (Giglione et al., Embo. J. 2000, 19, 5916-5929; Takeuchi et al., J. Biol. Chem. 2001, 276, 20064-20068; Takeuchi et al., J. Biol. Chem. 1998, 273, 15085-15090). The human mitochondrial Homo sapiens peptide deformylase (HsPDF) protein, which participates in the N-methionine excision pathway of newly synthesized peptides encoded by the mitochondrial genome, removes the N-terminal formyl group on the initiator methionine, and is important for cancer cell viability (Lee et al., Biochem. Biophys. Res. Commun. 2003, 312, 309-315; Lee et al., J. Clin. Invest. 2004, 114, 1107-1116; Serero et al., 2003 supra). For example, cancer cell lines appear to be more sensitive to HsPDF inhibition than normal non-cancer cell lines (Lee 2003 and Lee 2004 supra). As well, ATP depletion and mitochondrial membrane depolarization result from the inhibition of HsPDF with the PDF inhibitor actinonin. siRNA interference and pharmacologic inhibition both decrease human cell growth. Furthermore, the PDF inhibitor actinonin and its analogs exhibit anti-cancer activity in vitro and in vivo (Xu et al., Clin. Cancer Res. 1998, 4, 171-176).
As of today, most of the research for PDF inhibitors has been focused on the identification of bacterial PDF inhibitors. Nearly all bacterial PDF inhibitors currently in development share a common scaffold based on a peptidomimetic backbone linked to a chelating moiety (Jain et al., Curr. Med. Chem. 2005, 12, 1607-1621). Indeed, many of the reported screens were performed on small “rationally” designed libraries, often focused on chelator-based compounds (Gordon et al., Nature, 1962, 195, 701-702; Jain et al., Curr. Med. Chem. 2005, 12, 1607-1621; Clements et al., Antimicrob. Agents. Chemother. 2001, 45, 563-570). Issues related to the lack of selectivity of such compounds were recently highlighted (Turk et al., Nat. Rev. Drug Discov. 2006, 5, 785-799). Thus, there remains a need to identify PDF inhibitors structurally different from known bacterial PDF inhibitors, such that they might be selective for HsPDF. These observations led to a screen for novel non-peptidomimetic and non-hydroxamic acid based inhibitors of HsPDF as potentially new anti-proliferative agents.